[gmx-users] potential energy of a peptide in explicit DMSO

David spoel at xray.bmc.uu.se
Sun Jul 31 12:48:18 CEST 2005


On Thu, 2005-07-28 at 21:18 -0500, Xiaoming Zhang wrote:
> Yes, it is working!  Thanks.  
> I set those force constants to zero in dmso.itp and then rerun the md
> simulation.  The bonded energies seem reasonable.  After adding bonded
> and non-bonding energies all together, I got a positive potential
> energy (~700 kJ/mol) for peptide alone.  Is it normal to see the
> positive pot.E in gromacs?
> 
> I also have another question regarding the conformational transition
> during the md simulation.   I observed two major clusters of
> conformers during a 100ns simulation, cluster 1 has population ~80%
> and cluster 2 has ~15%.  I assume that the average potential energy of
> cluster 1 should be lower than cluster 2.  However, the calculated
> average potential energy of cluster 1 is ~10kJ/mole higher than that
> of cluster 2.  Does that mean I did the energy calculation
> incorrectly?

Populations are determined by the Gibbs energy.

It is non trivial to compute the potential energy of a protein in
solvent.

> 
> Thanks in advance for your help,
> xm
> 
> On 7/27/05, David <spoel at xray.bmc.uu.se> wrote:
> > On Wed, 2005-07-27 at 13:18 -0500, Xiaoming Zhang wrote:
> > > Thank you, David.  My solvent is DMSO.  I guess it will make
> > > contribution to bondeds?  If it does, then seems difficult to isolate
> > > the bonded energies for the peptide.
> > Yes. You could do it using -rerun and setting all the force constants
> > for DMSO to zero.
> > 
> > >
> > > xm
> > >
> > > On 7/27/05, David <spoel at xray.bmc.uu.se> wrote:
> > > > On Tue, 2005-07-26 at 22:14 -0500, Xiaoming Zhang wrote:
> > > > > Sorry, I should also include the bonded terms.  But those bondeds are
> > > > > for the whole system, aren't they?
> > > > yes, but if the rest is water there is no contribution to the bonded
> > > > energy.
> > > > > xm
> > > > >
> > > > > On 7/26/05, Xiaoming Zhang <smash04 at gmail.com> wrote:
> > > > > > Thanks a lot, Anton.  I simply changed the energy group in .mdp file
> > > > > > from "System" to "Protein" and then I can see some energy terms for
> > > > > > the protein when using g_energy.  However, I am confused about which
> > > > > > energy terms I should used to calculate the potential energy for the
> > > > > > peptide.  I searched the gromacs achieve and noticed that some other
> > > > > > users had the same confusion but no clear answer had been provided.
> > > > > > The following is my energy output from g_energy:
> > > > > >
> > > > > > **************************************************************************************
> > > > > > Select the terms you want from the following list
> > > > > > End your selection with 0
> > > > > >   1=          Bond   2=         Angle   3=   Proper Dih.   4=Ryckaert-Bell.
> > > > > >   5= Improper Dih.   6=         LJ-14   7=    Coulomb-14   8=       LJ (SR)
> > > > > >   9= Disper. corr.  10=  Coulomb (SR)  11=  Coulomb (LR)  12=     Potential
> > > > > >  13=   Kinetic En.  14=  Total Energy  15=   Temperature  16=Pressure (bar)
> > > > > >  17=         Box-X  18=         Box-Y  19=         Box-Z  20=        Volume
> > > > > >  21=  Density (SI)  22=            pV  23=        Vir-XX  24=        Vir-XY
> > > > > >  25=        Vir-XZ  26=        Vir-YX  27=        Vir-YY  28=        Vir-YZ
> > > > > >  29=        Vir-ZX  30=        Vir-ZY  31=        Vir-ZZ  32= Pres-XX (bar)
> > > > > >  33= Pres-XY (bar)  34= Pres-XZ (bar)  35= Pres-YX (bar)  36= Pres-YY (bar)
> > > > > >  37= Pres-YZ (bar)  38= Pres-ZX (bar)  39= Pres-ZY (bar)  40= Pres-ZZ (bar)
> > > > > >  41= #Surf*SurfTen  42=  Pcoupl-Mu-XX  43=  Pcoupl-Mu-YY  44=  Pcoupl-Mu-ZZ
> > > > > >  45=          Mu-X  46=          Mu-Y  47=          Mu-Z
> > > > > > 48=Coul-SR:Protein-Protein
> > > > > >  49=LJ:Protein-Protein  50=Coul-LR:Protein-Protein
> > > > > > 51=Coul-14:Protein-Protein  52=LJ-14:Protein-Protein
> > > > > >  53=Coul-SR:Protein-rest  54=LJ:Protein-rest  55=Coul-LR:Protein-rest
> > > > > >  56=Coul-14:Protein-rest
> > > > > >  57=LJ-14:Protein-rest  58=Coul-SR:rest-rest  59=  LJ:rest-rest
> > > > > > 60=Coul-LR:rest-rest
> > > > > >  61=Coul-14:rest-rest  62=LJ-14:rest-rest  63=      T-System  64=   Lamb-System
> > > > > > 48
> > > > > > 49
> > > > > > 50
> > > > > > 51
> > > > > > 52
> > > > > > 0
> > > > > >
> > > > > > Back Off! I just backed up energy.xvg to ./#energy.xvg.4#
> > > > > > Reading frame     70 time   35.000
> > > > > > Last frame read 76
> > > > > > WARNING: Incomplete frame: nr     77 time   38.000
> > > > > >
> > > > > >
> > > > > > Statistics over 37501 steps [ 0.0000 thru 37.5000 ps ], 5 data sets
> > > > > >
> > > > > > Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
> > > > > > -------------------------------------------------------------------------------
> > > > > > Coul-SR:Protein-Protein    -345.062    13.3941    12.7896  -0.367516   -13.7822
> > > > > > LJ:Protein-Protein         -33.7676    7.30473    7.02883  -0.183696   -6.88877
> > > > > > Coul-LR:Protein-Protein           0          0          0          0          0
> > > > > > Coul-14:Protein-Protein     719.375    9.16447    8.66907   0.274566    10.2965
> > > > > > LJ-14:Protein-Protein       71.2596    9.28124    9.27777 -0.0234419  -0.879095
> > > > > >
> > > > > > gcq#225: "Everybody is Smashing Things Down" (Offspring)
> > > > > >
> > > > > > ****************************************************************************************
> > > > > >
> > > > > > Is it correct to simply add up those five energies to get potential energy?
> > > > > >
> > > > > >
> > > > > > thanks,
> > > > > > xm
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 7/26/05, Anton Feenstra <feenstra at few.vu.nl> wrote:
> > > > > > > Xiaoming Zhang wrote:
> > > > > > >
> > > > > > > > Dear users,
> > > > > > > >
> > > > > > > > I am running the MD simulation of a cyclic peptide in explicit DMSO.
> > > > > > > > It is straightforward to retrieve the potential energy of the whole
> > > > > > > > system (peptide + DMSO) using g_energy.  However, I didn't find a way
> > > > > > > > to calculate/retrieve the potential energy for the peptide only.  I
> > > > > > > > was wondering if any of you had the experience and knew how to deal
> > > > > > > > with it.
> > > > > > >
> > > > > > > You need to define energy groups in your mdp file before you perform the
> > > > > > > simulation. Alternately, you can re-run your generated trajectory. See
> > > > > > > manual for more details.
> > > > > > >
> > > > > > > --
> > > > > > > Groetjes,
> > > > > > >
> > > > > > > Anton
> > > > > > >
> > > > > > > * NOTE: New Phone & Fax numbers (below) *
> > > > > > >
> > > > > > >  _____________ _______________________________________________________
> > > > > > > |             |                                                       |
> > > > > > > |  _   _  ___,| K. Anton Feenstra                                     |
> > > > > > > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > > > > > > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> > > > > > > | \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
> > > > > > > |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
> > > > > > > |             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
> > > > > > > |_____________|_______________________________________________________|
> > > > > > >
> > > > > >
> > > > > _______________________________________________
> > > > > gmx-users mailing list
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> > > > --
> > > > David.
> > > > ________________________________________________________________________
> > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > > > phone:  46 18 471 4205          fax: 46 18 511 755
> > > > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > >
> > > >
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> >
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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